GENETICS OF LACTASE PERSISTENCE IN SUDANESE POPULATIONS

Abstract

The aim of this study is to investigate the distribution of lactase phenotypes and known genotype and haplotypes associated with this trait in selected Sudanese pastorals (Beja, Fulani and Nilotes) as well as agro pastoralist (Nuba) and other group of agriculturalist (Hausa). Lactose tolerance test was done to assess the phenotype. A total of 298 blood and buccal samples have been collected and DNA was extracted. Two different PCR techniques were used; PCR-RFLP to detect -13910*T allele, and ARMS-PCR to detect the 5579 T/C and -678 A/G polymorphisms defining haplotypes A and C respectively. Our results showed variations in frequencies of the lactase persistence phenotype among Sudanese populations, with some association with their lifestyle (P = 0.01). The Nilotes however had low frequency of LCTP despite their known history of pastoralism. The -13910*T allele that is associated with lactase persistence in Finnish was absent in all Sudanese populations and was only found in 0.07 of the Fulani group. The genotype of the selected SNPs varied in frequencies between different groups. There was no association between the phenotype and genotypes of these SNPs (0.15 <P > 0.07) which were already in deviation from Hardy-Weinberg equilibrium. Based on Tajima’s test for selective neutrality the results suggest the presence of balancing selection, Tajima’s D values range from 1.3 to 2.3. There was no LD between different markers (D′ < 0.71). Some of the combined haplotypes are common to all groups while others are specific to particular lifestyle. Haplotype (CAC) is more frequent in pastoralists, while haplotype (CAT) is frequent in Hausa and Nuba who practice agriculture. In conclusion this trait is polymorphic and the absence of -13910*T allele suggest that it is not necessarily associated always with LCTP in different populations and that there might be another underlying polymorphism(s) to account for the LCTP consistent with recent findings of Mulcare et al (2004) and Tishkoff et al in (2006, submitted). We observe a signal of a haplotype (CAC) that shows with an elevated frequency in the pastoralists and that associates with LCTP (P = 0.03), suggesting that the main causative polymorphism in these groups might be in association with this haplotype.